Based on theoretical analysis and by using the micro data of 425 large-scale farmers in the major grain-producing regions of Anhui and Shandong provinces, the land plot consolidation effect of organization intervention in land transfer has been empirically studied by adopting OLS regression model and propensity score matching method. The research shows that organization intervention in land transfer has a significant effect on land plot consolidation. In the counterfactual framework, the average land plot size of large-scale farmers increases by 36.01 mu (with an increase rate of 72.60%) due to organization intervention. However, there is also some heterogeneity in the land plot consolidation effect of organization intervention in land transfer, which can only be applied when it is matched to farmers with lack of social capital and moderate scale of transfer. Therefore, the influence of system arrangement on the reconfiguration of rural land resources should be fully understood. It is necessary not only to adhere to the main line of market-oriented allocation of rural land resources and prevent excessive government intervention, but also to stimulate the vitality of villagers’ autonomy, strengthen the service organization construction and establish a standardized and targeted land transfer service system.